Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate GFF1569 PGA1_c15910 putative branched-chain amino acid transport ATP-binding protein
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__Phaeo:GFF1569 Length = 262 Score = 207 bits (528), Expect = 1e-58 Identities = 110/249 (44%), Positives = 161/249 (64%), Gaps = 1/249 (0%) Query: 18 LLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLF 77 +++ + L K FGG AVD A + + +GSITGLIGPNGAGKTTLFN+++ + P G V Sbjct: 1 MIVVEDLHKHFGGFHAVDGASLEIAKGSITGLIGPNGAGKTTLFNVIAGVLPPTSGRVTM 60 Query: 78 NGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQ 137 +G+ I L PH++ +G +RTFQ+A + +T EN+++ Q+GE +R+ Sbjct: 61 DGEDITGLPPHELFHKGLLRTFQIAHEFASMTCRENLMMVPGSQSGESLWNTWFGRKRIA 120 Query: 138 KEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGV 197 EERA R KA +LE + + A AG +SGGQ+KLLE+ R +M + K++ LDE AGV Sbjct: 121 DEERALRAKADEVLEFLTISHIADLKAGQVSGGQKKLLELGRTMMVDAKIVFLDEVGAGV 180 Query: 198 NPTLIGQICEHIVNWNRQ-GITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQSD 256 N TL+ I + I N + G TF+VIEH+M+ I LC V +AEG+ LA GT ++I+++ Sbjct: 181 NRTLLYTIADAIKRLNEERGYTFVVIEHDMEFIDRLCDPVICMAEGKKLAQGTLDEIKAN 240 Query: 257 PRVLEAYLG 265 +V+EAYLG Sbjct: 241 EQVIEAYLG 249 Lambda K H 0.319 0.136 0.389 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 194 Number of extensions: 14 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 267 Length of database: 262 Length adjustment: 25 Effective length of query: 242 Effective length of database: 237 Effective search space: 57354 Effective search space used: 57354 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory